[BioC] in-group missing arrayQualityMetrics()

[guest [guest]]

Hi I'm trying to run arrayQualityMetrics and I keep getting an error message saying that the intgroup is missing. However, I am very clearly specifying the intgroup and it definitely exists in my phenodata. I'm working with mogene.1.0.st.v1 arrays. Please see my error message and a few lines of my phenodata below:

Error message:

> arrayQualityMetrics(expressionset = dat, intgroup="SampleID",outdir = "QC_test", force =TRUE, do.logtransform = TRUE);
The directory 'QC_test' has been created.
Error in match(x, table, nomatch = 0L) : 
  argument "intgroup" is missing, with no default

phenodata:

> pData(dat)
                              ChipType SampleID MouseStrain       TumorOrigin
01_4T1_mouse1.CEL     MoGene-1_0-st-v1    4T1_1      Balb/c       Spontaneous
02_4T1_mouse2.CEL     MoGene-1_0-st-v1    4T1_2      Balb/c       Spontaneous
03_4T1_mouse3.CEL     MoGene-1_0-st-v1    4T1_3      Balb/c       Spontaneous
04_4T1_mouse4.CEL     MoGene-1_0-st-v1    4T1_4      Balb/c       Spontaneous
05_EMT-6_mouse1.CEL   MoGene-1_0-st-v1   EMT6_1      Balb/c       Spontaneous
06_EMT-6_mouse2.CEL   MoGene-1_0-st-v1   EMT6_2      Balb/c       Spontaneous

 
Any suggestions on how to fix this will be appreciated.

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] affyPLM_1.38.0             preprocessCore_1.24.0     
 [3] gcrma_2.34.0               affy_1.40.0               
 [5] arrayQualityMetrics_3.18.0 pd.mogene.1.0.st.v1_3.8.0 
 [7] RSQLite_0.11.4             DBI_0.2-7                 
 [9] oligo_1.26.0               Biobase_2.22.0            
[11] oligoClasses_1.24.0        BiocGenerics_0.8.0        

loaded via a namespace (and not attached):
 [1] affxparser_1.34.0    affyio_1.30.0        annotate_1.40.0     
 [4] AnnotationDbi_1.24.0 beadarray_2.12.0     BeadDataPackR_1.14.0
 [7] BiocInstaller_1.12.0 Biostrings_2.30.1    bit_1.1-11          
[10] Cairo_1.5-5          cluster_1.14.4       codetools_0.2-8     
[13] colorspace_1.2-4     ff_2.2-12            foreach_1.4.1       
[16] Formula_1.1-1        genefilter_1.44.0    GenomicRanges_1.14.4
[19] grid_3.0.2           Hmisc_3.13-0         hwriter_1.3         
[22] IRanges_1.20.6       iterators_1.0.6      lattice_0.20-24     
[25] latticeExtra_0.6-26  limma_3.18.7         plyr_1.8            
[28] RColorBrewer_1.0-5   reshape2_1.2.2       setRNG_2011.11-2    
[31] splines_3.0.2        stats4_3.0.2         stringr_0.6.2       
[34] survival_2.37-4      SVGAnnotation_0.93-1 vsn_3.30.0          
[37] XML_3.98-1.1         xtable_1.7-1         XVector_0.2.0       
[40] zlibbioc_1.8.0      
> 


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